Crystal structure of pegylated plastocyanin at 4.2 a resolution

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 42% strand (DSSP).

Ligands and binding sites

• LCY · 1-methylpyrrolidine-2,5-dione · ligand · 4 copies · chains A, B, C, D
• CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 520 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 513 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 454 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 423 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 231 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 4R0O · Crystal structure of PEGylated plastocyanin at 4.2 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
• Q51883 · AlphaFold monomer V2.0 prediction for plastocyanin (Q51883) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q51883
• Elsewhere: RCSB PDB 4R0O · PDBe 4R0O · UniProt Q51883